{"id":4304,"date":"2017-10-12T11:33:58","date_gmt":"2017-10-12T11:33:58","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=4304"},"modified":"2017-10-12T11:33:58","modified_gmt":"2017-10-12T11:33:58","slug":"salmon","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/salmon\/","title":{"rendered":"Salmon"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"http:\/\/salmon.readthedocs.io\/en\/latest\/\">Salmon<\/a> is a tool for wicked-fast transcript quantification from RNA-seq data. It requires a set of target transcripts (either from a reference or de-novo assembly) to quantify. All you need to run Salmon is a FASTA file containing your reference transcripts and a (set of) FASTA\/FASTQ file(s) containing your reads. Optionally, Salmon can make use of pre-computed alignments (in the form of a SAM\/BAM file) to the transcripts rather than the raw reads.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>None (GPLv3+ licensed.)<\/p>\n<h2>Set up procedure<\/h2>\n<p>To access the software you must first load the modulefile:<\/p>\n<pre>module add apps\/gcc\/salmon\/0.8.2<\/pre>\n<h2>Running the application<\/h2>\n<p>Salmon is multi-threaded, so should be run in the <a href=\"http:\/\/ri.itservices.manchester.ac.uk\/csf2\/batch\/parallel-jobs\/\">smp.pe parallel environment<\/a>.  See the <a href=\"http:\/\/salmon.readthedocs.io\/en\/latest\/salmon.html#using-salmon\">documentation<\/a> concerning the appropriate number of threads to use (i.e. slots to request).<\/p>\n<h2>Further Information<\/h2>\n<p><a href=\"http:\/\/salmon.readthedocs.io\/en\/latest\/\">Salmon web site<\/a> <\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. It requires a set of target transcripts (either from a reference or de-novo assembly) to quantify. All you need to run Salmon is a FASTA file containing your reference transcripts and a (set of) FASTA\/FASTQ file(s) containing your reads. Optionally, Salmon can make use of pre-computed alignments (in the form of a SAM\/BAM file) to the transcripts rather than the raw reads. Restrictions.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/salmon\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":20,"featured_media":0,"parent":31,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-4304","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4304","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/users\/20"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/comments?post=4304"}],"version-history":[{"count":2,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4304\/revisions"}],"predecessor-version":[{"id":4306,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4304\/revisions\/4306"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/31"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/media?parent=4304"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}